initDGEobj {DGEobj}

Initialize with base data (primaryAssayData, row annotations, col annotations)

Description

Initialize with base data (primaryAssayData, row annotations, col annotations)

Usage

initDGEobj(
  primaryAssayData,
  rowData,
  colData,
  level,
  customAttr,
  allowShortSampleIDs = FALSE,
  DGEobjDef = initDGEobjDef()
)

Arguments

primaryAssayData

A numeric matrix or dataframe with row and colnames. Each column represents a sample. Each row represents and assay. This is typically the counts matrix in a DGE RNA-Seq experiment.

rowData

Gene, exon, isoform or protein level annotation. Rownames must match the rownames in primaryAssayData

colData

A dataframe describing the experiment design. Rownames much match the colnames(primaryAssayData)

level

One of "gene", "exon", "isoform" or "protein"

customAttr

(optional) Named list of attributes

allowShortSampleIDs

Using sequential integer rownames (even if typed as character) is discouraged and by default will abort the DGEobj creation. If you have a legitimate need to have short sample names composed of numeric characters, you can set this argument to TRUE (default = FALSE)

DGEobjDef

An object definition. Defaults to the global DGEobj definition (initDGEobjDef()) and you usually shouldn't change this unless you're customizing the object for new data types.

Value

A DGEobj

Examples

   dgeObj   <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
   MyCounts <- dgeObj$counts
   geneinfo <- dgeObj$geneData
   sampinfo <- dgeObj$design

  myDgeObj <- initDGEobj(primaryAssayData = MyCounts,
                         rowData          = geneinfo,
                         colData          = sampinfo,
                         level            = "gene",
                         customAttr       = list (Genome = "Rat.B6.0",
                                               GeneModel = "Ensembl.R89"))